Molecular phylogeny of the family Bacillariaceae based on 18S rDNA sequences: focus on freshwater Nitzschia of the section Lanceolatae

Sequence analysis of the 18S rDNA gene from 93 taxa belonging to the pennate diatoms plus one centric, Cyclotella meneghiniana Kutzing, were made using two different alignments (Clustal and secondary structure) and two different types of algorithms (neighbour-joining and maximum likelihood). The monophyly of the bacillariacean taxa depends on the type of alignment used for the 18S gene. A secondary structure alignment does not support its monophyly, whereas a Clustal alignment does, but only in the maximum likelihood analysis. The Eunotiales were basal to all other raphid diatoms if a maximum likelihood analysis was used, regardless of the alignment, whereas a neighbour-joining analysis, regardless of the alignment, pulled the Eunotiales inside the raphid diatom sister to one of the bacillariophycean clades in the secondary structure alignment and sister to a monophyletic bacillariophycean clade in the Clustal alignment. The classification of the Bacillariaceae by Krammer & Lange-Bertalot and Round, Crawford & Mann was not supported by the 18S phylogeny. Taxa of the section Lanceolatae Grunow were present in different clades, but sister relationships between well-supported clades were not supported. Multiseriate striae, which are often considered an important feature, were not supported as being clade-defining features. The two groups, A and B of Krammer & Lange-Bertalot in the section Lanceolatae were not supported by the phylogenetic analyses.